Missouri has access to over 1,000 miles of the Missouri and Mississippi Rivers, more than the combined length of Interstates 44, 55 and 70 combined. These natural assets are a vital link in Missouri’s transportation chain. Over 500 million tons of cargo flow on these rivers annually; that is the equivalent of 19 million trucks on the highways.

Missouri Statute Chapter 68 RSMo allows for the formation of port authorities, and the department's waterways unit assists authorized cities and counties in forming port authorities to foster local economic development. MoDOT’s waterways staff promotes the use of Missouri's navigable rivers to make low-cost waterborne transportation benefits available to business. It also assists in capital and administrative funding, acts as an informational clearinghouse, provides technical assistance and represents port interests within industrial and governmental circles. MoDOT’s waterways section also provides assistance and funding to two Mississippi River ferry crossings at Ste. Genevieve and Dorena.